Enable delivery of external samples (#2727)(patch)

Externally sequenced samples do not have reads assigned to them in status db, which means the deliver command failed for them. This change enables delivering samples associated with an application that is marked as external are possible to deliver.

cg/meta/deliver.py

@@ -100,7 +100,7 @@ def deliver_files(self, case_obj: Case):
 
         link: CaseSample
         for link in links:
-            if link.sample.sequencing_qc or self.deliver_failed_samples:
+            if self.sample_is_deliverable(link):
                 sample_id: str = link.sample.internal_id
                 sample_name: str = link.sample.name
                 LOG.debug(f"Fetch last version for sample bundle {sample_id}")
@@ -123,6 +123,12 @@ def deliver_files(self, case_obj: Case):
                 f"Sample {link.sample.internal_id} did not receive enough reads and will not be delivered"
             )
 
+    def sample_is_deliverable(self, link: CaseSample) -> bool:
+        sample_is_external: bool = link.sample.application_version.application.is_external
+        deliver_failed_samples: bool = self.deliver_failed_samples
+        sample_passes_qc: bool = link.sample.sequencing_qc
+        return sample_passes_qc or deliver_failed_samples or sample_is_external
+
     def deliver_case_files(
         self, case_id: str, case_name: str, version: Version, sample_ids: set[str]
     ) -> None: